AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_mixed5_hpyl_reg_300.orf -o320_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP01145 214 AE000511 #2 RHP01148 64 AE000511 #3 RHP01149 66 AE000511 #4 RHP00049 77 AE000511 #5 RHP00050 34 AE000511 #6 RHP00589 61 AE000511 Motif number 1 ATTTTGAGTTTTTAGGAGCAGTTTTT 1 3 0 TTTAGGATTT 0.975045 -212 GTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAG 1 22 0 TTTAGGATTT 0.975045 -193 TGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAG 1 50 0 TTAAGGTTTT 0.922778 -165 TTCTACTACATTTGAAATAATTTTTCTTATAAAC 1 74 1 TTTGAAATTT 0.917271 -141 TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAA 1 94 0 TTTAGGTTTT 0.96516 -121 CAATAGCCCCTTTGAATTGAATTTTTTCTCAATT 1 116 0 TTTGAAATTT 0.917271 -99 GGGCTATTGTTTAAAATTTACATTTTTTAAACGC 1 141 1 TTAAAAAATT 0.880041 -74 ATTTACATTTTTTAAACGCTATTAGATATAATAA 1 156 1 TTTAAATTTA 0.874861 -59 ATTGTCCTTATTAAAATAATCATTCGTATTCAAA 2 39 0 TTAAAATATT 0.838749 -26 AAAAATATTTTAAGGGTAATATTTTAAAAAAT 3 9 1 TTTAAGATAT 0.868449 -58 AGGGTAATATTTTAAAAAATTTTTGTATAATCAA 3 23 1 TTTAAATTTT 0.955777 -44 CCTAATTTAGTTTAAAAGGTTTTTACAAAC 4 7 0 TTTAAATTTT 0.955777 -71 TTAAACTAAATTAGGGTAGTATTATAGCATTTAA 4 26 1 TTAGGGTTTA 0.584611 -52 TTGATAGGGCTTTAGGGGAAAATAG 4 63 1 TTTAGGAATA 0.87591 -15 TCCCTTTAAATTAAAACAAAAATTAAAT 5 5 0 TTAAAAAATT 0.880044 -30 TTTGTTTTAATTTAAAGGGATAAAAC 5 19 1 TTTAAAAAAA 0.453596 -16 TTTTAAAGATTTTAAGCTAAAATTTTAGCATACA 6 22 1 TTTAAGAATT 0.960647 -40 ****** * *** Masking position 2 Map Score: 22.2293 Number of sites scoring better than the average of aligned sites = 2326 Number in coding regions = 1819 Number in noncoding regions = 507 Number of orfs with sites within 600 bp upstream = 295 Fraction of orfs with sites within 600 bp upstream = 0.0473819 Motif number 2 CTACTACATTTGAAATAATTTTTCTTATAA 1 76 1 TGAAATAATT 0.868847 -139 ACCTAAATTGAGAAAAAATTCAATTCAAAG 1 111 1 AGAAAAAATT 0.936054 -104 AAACGCTATTAGATATAATAAGGGATAGTT 1 169 1 AGATATAATA 0.907542 -46 GAATGAAATAAGCTATAATAAGCCCATTTT 2 12 1 AGCTATAATA 0.958849 -53 AAAAATATTTTAAGGGTAAT 3 1 1 AAAAATATTT 0.605376 -66 TTGTTGATTATACAAAAATTTTTTAAAATA 3 30 0 TACAAAAATT 0.868905 -37 AAACCTTTTAAACTAAATTAGGGTAGTATT 4 19 1 AACTAAATTA 0.7331 -59 AAAGATTAAATGCTATAATACTACCCTAAT 4 35 0 TGCTATAATA 0.91372 -43 TTTAAATTAAAACAAAAATTAAAT 5 5 0 AACAAAAATT 0.936043 -30 AAAGATTTTAAGCTAAAATTTTAGCATACA 6 26 1 AGCTAAAATT 0.971659 -36 ********** Masking position 5 Map Score: 8.30949 Number of sites scoring better than the average of aligned sites = 962 Number in coding regions = 793 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 3 AAATTAACCTAAAATCGCTTGACGCAAAAA 1 33 1 AAAATCGCTT 0.838082 -182 AATTTTAAACAATAGCCCCTTTGAATTGAA 1 129 0 AATAGCCCCT 0.985788 -86 ATAGGTGGTAACTATCCCTTATTATATCTA 1 178 0 ACTATCCCTT 0.974673 -37 ATAAGCTATAATAAGCCCATTTTGAATACG 2 19 1 ATAAGCCCAT 0.877356 -46 TTTTTTAAAATATTACCCTTAAAATATTTT 3 12 0 TATTACCCTT 0.776777 -55 CTATTTTCCCCTAAAGCCCTAT 4 66 0 ATTTTCCCCT 0.941731 -12 GTTTTATCCCTTTAAATTAAAA 5 23 0 TTTATCCCTT 0.960028 -12 CAATAGCCCTTTTTTAAAGAT 6 2 1 AATAGCCCTT 0.990248 -60 ********** Masking position 10 Map Score: 5.8504 Number of sites scoring better than the average of aligned sites = 930 Number in coding regions = 820 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 4 CTAAAAACTCAAAATTAACCTAAAATCGCTT 1 22 1 AAAATTACCT 0.985475 -193 GCTATTGTTTAAAATTTACATTTTTTAAACG 1 143 1 AAAATTTCAT 0.921206 -72 TACCACCTATAAAATAAGGATCGTTCA 1 198 1 AAAATAAGAT 0.824848 -17 TGTCCTTATTAAAATAATCATTCGTATTCAA 2 40 0 AAAATAACAT 0.960419 -25 AATTTTTTAAAATATTACCCTTAAAATATTT 3 13 0 AATATTACCT 0.981205 -54 TAAATGCTATAATACTACCCTAATTTAGTTT 4 28 0 AATACTACCT 0.941419 -50 TTTAAGCTAAAATTTTAGCATACAAATACAA 6 32 1 AATTTTACAT 0.899781 -30 ******* *** Masking position 2 Map Score: 4.4254 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 189 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 TTTTGCGTCAAGCGATTTTAGGTTAATTTT 1 32 0 AGCGATTTTA 0.78256 -183 GAATTAAGGCAGTGTTTTTGCGTCAAGCGA 1 47 0 AGTGTTTTTG 0.883296 -168 TCAATTCAAAGGGGCTATTGTTTAAAATTT 1 130 1 GGGGCTATTG 0.97714 -85 ACATTTTTTAAACGCTATTAGATATAATAA 1 160 1 AACGCTATTA 0.903786 -55 TATTCAAAATGGGCTTATTATAGCTTATTT 2 17 0 GGGCTTATTA 0.653464 -48 TTTAGTTTAAAAGGTTTTTACAAAC 4 6 0 AAGGTTTTTA 0.875976 -72 TCAAAGATTAAATGCTATAATACTACCCTA 4 37 0 AATGCTATAA 0.657421 -41 AATCTTTGATAGGGCTTTAGGGGAAAATAG 4 58 1 AGGGCTTTAG 0.957319 -20 TCTTTAAAAAAGGGCTATTG 6 1 0 AGGGCTATTG 0.988694 -61 ********** Masking position 6 Map Score: 4.38473 Number of sites scoring better than the average of aligned sites = 2539 Number in coding regions = 2319 Number in noncoding regions = 220 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 6 ********** No masking Map Score: -5.94424e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: -5.94424e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: -5.94424e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0